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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Quantifying electron cyclotron power deposition broadening in DIII-D and the potential consequences for the ITER EC system

Abstract The injection of electron cyclotron (EC) waves fulfills a number of important tasks in nuclear fusion devices for which detailed knowledge of the spatial power deposition profile is critical. This deposition profile is commonly determined using forward models such as beam or ray tracing. Recent numerical and experimental studies have shown that small-angle scattering of the EC beam as it passes through the turbulent plasma edge can cause significant broadening of the effective deposition profile, leading to considerable underestimation of the deposition width by forward methods. However, traditional inverse methods to determine the deposition profile from measurements overestimate the deposition profile width due to transport broadening. In this work, we implement three novel methods to resolve the EC power deposition profile from measurements that counteract transport broadening by simultaneously resolving transport and power deposition. We validate their assumptions and compare the results from these methods to the traditional break-in-slope method as well as to the TORAY ray-tracing code in a set of DIII-D discharges spanning five different confinement modes. We show that the four different inverse methods, novel and established, paint a consistent picture of deposition broadening. Specifically, we show that the measured power deposition profile is between 1.6 and 3.6 times wider than the TORAY profiles. Moreover, we show the considerable consequences that this level of broadening can have for ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Cross-section measurement of the 82 Kr ($p,γ$) 83 Rb reaction in inverse kinematics

The total cross section of the 82 Kr(p,γ) 83 Rb reaction was measured for the first time at effective center-of-mass energies between 2.4 and 3.0 MeV, within the relevant Gamow window for the astrophysical γ process. The experiment took place at the National Superconducting Cyclotron Laboratory at Michigan State University using the ReA facility. A 82 Kr beam was directed onto a hydrogen gas cell located at the center of the Summing NaI(Tl) (SuN) detector. Here, the obtained spectra were analyzed using the γ-summing technique and the extracted cross section was compared to standard statistical model calculations using the non-smoker and talys codes. The comparison indicates that standard statistical model calculations tend to overproduce the cross section of the 82 Kr(p,γ) 83 Rb reaction relative to the experimentally measured values. Furthermore, the experimental data were used to provide additional constraints on the nuclear level density and the γ-ray strength function used in the statistical model calculations.

59 ≤ A ≤ 89↗
DOE OSTI2021

Nonuniform Absorption and Scattered Light in Direct-Drive Implosions Driven by Polarization Smoothing

Laser-direct-drive symmetric implosions on OMEGA illuminate a target with 60 laser beams and are designed to produce spherical implosions. Each beam is smoothed using orthogonal polarizations obtained by passing through distributed polarization rotators (DPR’s). Observations of the scattered light from OMEGA implosions do not show the expected symmetry and have much larger variation than standard predictions. For the first time, we have quantified the scattered-light nonuniformity from individual beams and identified the DPR’s as the source of the enhanced nonuniformity. An instrument was invented that isolated and measured the variation in the intensity and polarization of the light scattered from each OMEGA beam. The asymmetric intensity and polarization measurements are explained when the on-target offsets between the two orthogonal polarizations produced by the DPR’s are modeled using a 3-D cross-beam energy transfer (CBET) code that tracks the polarizations of each beam. The time-integrated nonuniformity in laser absorption and scattered light due to CBET and the DPR polarization offsets during high-performance OMEGA implosions is predicted to be significant and dominated by low spherical harmonic mode numbers. Further, the nonuniformity is predicted to be greatly reduced by replacing the DPR’s with new optics that create smaller offsets.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

MatRIS: Multi-level Math Library Abstraction for Heterogeneity and Performance Portability using IRIS Runtime

Vendor libraries are tuned for a specific architecture and are not portable to others. Moreover, they lack support for heterogeneity and multi-device orchestration, which is required for efficient use of contemporary HPC and cloud resources. To address these challenges, we introduce MatRIS—a multilevel math library abstraction for scalable and performance-portable sparse/dense BLAS/LAPACK operations using IRIS runtime. The MatRIS-IRIS co-design introduces three levels of abstraction to make the implementation completely architecture agnostic and provide highly productive programming. We demonstrate that MatRIS is portable without any change in source code and can fully utilize multi-device heterogeneous systems by achieving high performance and scalability on Summit, Frontier, and a CADES cloud node equipped with four NVIDIA A100 GPUs and four AMD MI100 GPUs. A detailed performance study is presented in which MatRIS demonstrates multi-device scalability. When compared, MatRIS provides competitive and even better performance than libraries from vendors and other third parties.

Monil, M. A. H.↗
DOE OSTI2025

An experimentally informed design process for future inertial confinement fusion facilities

The achievement of ignition in the laboratory has renewed interest in defining the requirements for a future high-gain inertial confinement fusion (ICF) facility. Our best chance of predicting future ICF performance is with 3-D radiation hydrodynamic simulations that have been benchmarked against experimental data, but their high computational cost is prohibitive for use in practical design studies. We introduce a hierarchical approach where 3-D simulations are tuned to match experimental measurements and used to train 3-D degradation models in 1-D simulations allowing for accurate predictions over the entire OMEGA direct-drive database. A genetic algorithm was used in combination with the trained 1-D simulations to search for optimal direct-drive implosion designs at driver energies ranging from 20 kJ to 10 MJ. As the fidelity of 3-D codes improves, this approach will provide a viable experimentally informed tool for defining the next ICF facility.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Expanded Validation of Uranium Systems with the KENO Monte Carlo Codes and SCALE 6.2.4 [Slides]

There is likely a trend in bias for uranium-fueled systems as a function of spectrum, but probably not as a function of enrichment. Some enrichment trends appear, but are potentially the result of outlier experimental results; further investigation is needed where possible. There are good examples in this data of markedly different biases from different systems. Future work includes review and vetting for inclusion in the VALID library and analysis with TSUNAMI.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

DMFTwDFT: An open-source code combining Dynamical Mean Field Theory with various density functional theory packages

We report Dynamical Mean Field Theory (DMFT) is a successful method to compute the electronic structure of strongly correlated materials, especially when it is combined with density functional theory (DFT). Here, we present an open-source computational package (and a library) combining DMFT with various DFT codes interfaced through the Wannier90 package. The correlated subspace is expanded as a linear combination of Wannier functions introduced in the DMFT approach as local orbitals. In particular, we provide a library mode for computing the DMFT density matrix. This library can be linked and then internally called from any DFT package, assuming that a set of localized orbitals can be generated in the correlated subspace. The existence of this library allows developers of other DFT codes to interface with our package and achieve the charge-self-consistency within DFT+DMFT loops. To test and check our implementation, we computed the density of states and the band structure of well-known solid-state correlated materials, namely LaNiO, SrVO, and NiO. The obtained results are compared to those obtained from other DFT+DMFT implementations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Radial electric field and density fluctuations measured by Doppler reflectometry during the post-pellet enhanced confinement phase in W7-X

Radial profiles of density fluctuations and the radial electric field, Er, have been measured using Doppler reflectometry during the post-pellet enhanced confinement phase achieved, under different heating power levels and magnetic configurations, during the 2018 W7-X experimental campaign. A pronounced Er-well is measured with local values as high as -40 kV m -1 in the radial range ρ ~ 0.7–0.8 during the post-pellet enhanced confinement phase. The maximum Er intensity scales with both the plasma density and electron cyclotron heating power level, following a similar trend to the plasma energy content. A good agreement is found when the experimental Er profiles are compared to simulations carried out using the neoclassical codes, the drift kinetic equation solver (DKES) and kinetic orbit-averaging solver for stellarators (KNOSOS). The density fluctuation level decreases from the plasma edge toward the plasma core and the drop is more pronounced in the post-pellet enhanced confinement phase than in reference gas-fuelled plasmas. Besides, in the post-pellet phase, the density fluctuation level is lower in the high iota magnetic configuration than in the standard one. Therefore, to determine whether this difference is related to the differences in the plasma profiles or to the stability properties of the two configurations, gyrokinetic simulations have been carried out using the codes stella and EUTERPE. The simulation results point to the plasma profile evolution after the pellet injection and the stabilization effect of the radial electric field profile as the dominant players in the stabilization of the plasma turbulence.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Quantification of the effect of uncertainty on impurity migration in PISCES-A simulated with GITR

A Bayesian inference strategy has been used to estimate uncertain inputs to global impurity transport code (GITR) modeling predictions of tungsten erosion and migration in the linear plasma device, PISCES-A. This allows quantification of GITR output uncertainty based on the uncertainties in measured PISCES-A plasma electron density and temperature profiles (n e , T e ) used as inputs to GITR. The technique has been applied for comparison to dedicated experiments performed for high (4 × 10 22 m –2 s –1 ) and low (5 × 10 21 m –2 s –1 ) flux 250 eV He–plasma exposed tungsten (W) targets designed to assess the net and gross erosion of tungsten, and corresponding W impurity transport. The W target design and orientation, impurity collector, and diagnostics, have been designed to eliminate complexities associated with tokamak divertor plasma exposures (inclined target, mixed plasma species, re-erosion, etc) to benchmark results against the trace impurity transport model simulated by GITR. The simulated results of the erosion, migration, and re-deposition of W during the experiment from the GITR code coupled to materials response models are presented. Specifically, the modeled and experimental W I emission spectroscopy data for a 429.4 nm line and net erosion through the target and collector mass difference measurements are compared. Furthermore, the methodology provides predictions of observable quantities of interest with quantified uncertainty, allowing estimation of moments, together with the sensitivities to plasma temperature and density.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

On the role of ion temperature gradient turbulence in driving ion thermal transport in neutral beam injection-heated L-mode plasmas in a superconducting tokamak

In this paper, we report a detailed experimental study of the role of ion-temperature-gradient driven turbulence in driving ion thermal transport in neutral beam injection (NBI)-heated L-mode plasmas in Experimental Advanced Superconducting Tokamak (EAST) (Wan et al 2000 Nucl. Fusion 40 1057) coupled with linear and nonlinear gyrokinetic simulations. Significant ion-scale turbulence k ⟂ < cm −1 (k ⟂ < 1.5, where k ⟂ where is the perpendicular wavenumber and ρ s is the ion gyroradius calculated using local electron temperature T e ), measured with a microwave reflectometer, is observed in the plasma core at for r/a ≈ 0.265 and 0.5 (where r is half the diameter of the closed flux surface at a given radial position, and a is half the diameter of the last closed flux surface). Local linear stability analysis with experimental equilibrium quantities at these two radial locations using the GS2 gyrokinetic code shows that the most unstable ion-scale micro-instability is the ion temperature gradient (ITG) mode. Since the computed maximum ion-scale linear growth rates are larger than the local Waltz-Miller E × B shearing rate (Waltz and Miller 1999 Phys. Plasmas 6 4265), the E × B shear is unable to suppress ion-scale turbulence, consistent with the experimental observation of ion-scale turbulence. Experimental ion and electron thermal transports, calculated with power balance analysis, are both anomalous with ion thermal transport being the dominant channel. Nonlinear gyrokinetic simulations using the electrostatic global particle-in-cell gyrokinetic tokamak simulation (GTS) code (Weixing Wang et al 2010 Phys. Plasmas 17 072511) show good quantitative agreement between predicted ion thermal transport and that from the power balance analysis. These results demonstrate for the first time the important role of ITG turbulence in driving thermal transport in NBI-heated L-mode plasmas in EAST, showing the effectiveness of GTS code in simulating electrostatic turbulence in EAST and the need of suppressing ITG turbulence to improve energy confinement in EAST.

Sun, P. J. [Chinese Academy of Sciences (CAS), Hef↗
DOE OSTI2026

Multimodal Approaches for Leveraging Domain Knowledge with State-of-the-Art Machine Learning to Engineer Biocatalysts

This grant aimed to accelerate the development of specialized enzymes—biological catalysts essential for sustainable manufacturing and medicine—by integrating traditional laboratory evolution with cutting-edge artificial intelligence. To achieve this, we developed a suite of high-throughput sequencing tools and a centralized database to bridge the gap between a protein’s genetic "code" and its physical function. By training machine learning models on large datasets, we also demonstrated the ability to move beyond slow, trial-and-error testing to a "generative" approach, where AI can independently design new, versatile enzymes like tryptophan synthases. Ultimately, these findings demonstrate that combining laboratory data with computer-guided design enables the engineering of highly efficient biological tools with unprecedented speed and precision.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations

Background: Short-term forecasts of infectious disease burden can contribute to situational awareness and aid capacity planning. Based on best practice in other fields and recent insights in infectious disease epidemiology, one can maximise the predictive performance of such forecasts if multiple models are combined into an ensemble. Here, we report on the performance of ensembles in predicting COVID-19 cases and deaths across Europe between 08 March 2021 and 07 March 2022. Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance. Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast models. Conclusions: Our results support the use of combining forecasts from individual models into an ensemble in order to improve predictive performance across epidemiological targets and populations during infectious disease epidemics. Our findings further suggest that median ensemble methods yield better predictive performance more than ones based on means. Our findings also highlight that forecast consumers should place more weight on incident death forecasts than incident case forecasts at forecast horizons greater than 2 weeks. Funding: AA, BH, BL, LWa, MMa, PP, SV funded by National Institutes of Health (NIH) Grant 1R01GM109718, NSF BIG DATA Grant IIS-1633028, NSF Grant No.: OAC-1916805, NSF Expeditions in Computing Grant CCF-1918656, CCF-1917819, NSF RAPID CNS-2028004, NSF RAPID OAC-2027541, US Centers for Disease Control and Prevention 75D30119C05935, a grant from Google, University of Virginia Strategic Investment Fund award number SIF160, Defense Threat Reduction Agency (DTRA) under Contract No. HDTRA1-19-D-0007, and respectively Virginia Dept of Health Grant VDH-21-501-0141, VDH-21-501-0143, VDH-21-501-0147, VDH-21-501-0145, VDH-21-501-0146, VDH-21-501-0142, VDH-21-501-0148. AF, AMa, GL funded by SMIGE - Modelli statistici inferenziali per governare l'epidemia, FISR 2020-Covid-19 I Fase, FISR2020IP-00156, Codice Progetto: PRJ-0695. AM, BK, FD, FR, JK, JN, JZ, KN, MG, MR, MS, RB funded by Ministry of Science and Higher Education of Poland with grant 28/WFSN/2021 to the University of Warsaw. BRe, CPe, JLAz funded by Ministerio de Sanidad/ISCIII. BT, PG funded by PERISCOPE European H2020 project, contract number 101016233. CP, DL, EA, MC, SA funded by European Commission - Directorate-General for Communications Networks, Content and Technology through the contract LC-01485746, and Ministerio de Ciencia, Innovacion y Universidades and FEDER, with the project PGC2018-095456-B-I00. DE., MGu funded by Spanish Ministry of Health / REACT-UE (FEDER). DO, GF, IMi, LC funded by Laboratory Directed Research and Development program of Los Alamos National Laboratory (LANL) under project number 20200700ER. DS, ELR, GG, NGR, NW, YW funded by National Institutes of General Medical Sciences (R35GM119582; the content is solely the responsibility of the authors and does not necessarily represent the official views of NIGMS or the National Institutes of Health). FB, FP funded by InPresa, Lombardy Region, Italy. HG, KS funded by European Centre for Disease Prevention and Control. IV funded by Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS) through contract 2021-021OE. JDe, SMo, VP funded by Netzwerk Universitatsmedizin (NUM) project egePan (01KX2021). JPB, SH, TH funded by Federal Ministry of Education and Research (BMBF; grant 05M18SIA). KH, MSc, YKh funded by Project SaxoCOV, funded by the German Free State of Saxony. Presentation of data, model results and simulations also funded by the NFDI4Health Task Force COVID-19 ( https://www.nfdi4health.de/task-force-covid-19-2 ) within the framework of a DFG-project (LO-342/17-1). LP, VE funded by Mathematical and Statistical modelling project (MUNI/A/1615/2020), Online platform for real-time monitoring, analysis and management of epidemic situations (MUNI/11/02202001/2020); VE also supported by RECETOX research infrastructure (Ministry of Education, Youth and Sports of the Czech Republic: LM2018121), the CETOCOEN EXCELLENCE (CZ.02.1.01/0.0/0.0/17-043/0009632), RECETOX RI project (CZ.02.1.01/0.0/0.0/16-013/0001761). NIB funded by Health Protection Research Unit (grant code NIHR200908). SAb, SF funded by Wellcome Trust (210758/Z/18/Z).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Edge ICRF simulations in 3D geometry: From MHD equilibrium to coupling determination

We present in this work a consistent numerical scheme that allows the computation of 3D magnetic fields a nd 3D density profiles and their usage in ion cyclotron range of frequencies (ICRF) coupling simulations. We first utilize the PARVMEC code to compute the 3D free-boundary plasma equilibrium in the ideal magnetohydrodynamic (MHD) approximation. Since the PARVMEC solution is only defined within the last closed flux surface (LCFS), the magnetic field domain is extended to the scrape-off layer (SOL) via the BMW code, which computes a divergence-free magnetic field solution arising from the external conductors’ vacuum field a nd t he PARVMEC flux surface currents. This magnetic reconstruction is then used in the EMC3-EIRENE transport code in order to compute 3D density profiles. In the last step, the RAPLICASOL code is utilized to compute the ICRF antenna S-matrices resulting from the 3D density profiles. We exemplify this scheme for the ASDEX Upgrade tokamak. A new implementation of a curved model for the ASDEX Upgrade ICRF 2-strap antenna in RAPLICASOL allows simulations in realistic geometry, without any coordinate transformations.

Lopez, Graham↗
DOE OSTI2021

Exosphere Modeling of Proxima b: A Case Study of Photochemical Escape with a Venus-like Atmosphere

Exoplanets orbiting M dwarfs within habitable zones are exposed to stellar environments more extreme than that terrestrial planets experience in our solar system, which can significantly impact the atmospheres of the exoplanets and affect their habitability and sustainability. This study provides the first prediction of hot oxygen corona structure and the associated photochemical loss from a 1 bar CO 2 -dominated atmosphere of a Venus-like rocky exoplanet, where dissociative recombination of O 2 + ions is assumed to be the major source reaction for the escape of neutral O atoms and formation of the hot O corona (or exospheres) as on Mars and Venus. We employ a 3D Monte Carlo code to simulate the exosphere of Proxima Centauri b (PCb) based on the ionosphere simulated by a 3D magnetohydrodynamic model. Our simulation results show that variability of the stellar wind dynamic pressure over one orbital period of PCb does not affect the overall spatial structure of the hot O corona but contributes to the change in the global hot O escape rate that varies by an order of magnitude. The escape increases dramatically when the planet possesses its intrinsic magnetic fields as the ionosphere becomes more extended with the presence of a global magnetic field. Furthermore, the extended hot O corona may lead to a more extended H exosphere through collisions between thermal H and hot O, which exemplifies the importance of considering nonthermal populations in exospheres to interpret future observations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Statistical data analysis of x-ray spectroscopy data enabled by neural network accelerated Bayesian inference

Bayesian inference applied to x-ray spectroscopy data analysis enables uncertainty quantification necessary to rigorously test theoretical models. However, when comparing to data, detailed atomic physics and radiation transfer calculations of x-ray emission from non-uniform plasma conditions are typically too slow to be performed in line with statistical sampling methods, such as Markov Chain Monte Carlo sampling. Furthermore, differences in transition energies and x-ray opacities often make direct comparisons between simulated and measured spectra unreliable. Here, we present a spectral decomposition method that allows for corrections to line positions and bound–bound opacities to best fit experimental data, with the goal of providing quantitative feedback to improve the underlying theoretical models and guide future experiments. In this work, we use a neural network (NN) surrogate model to replace spectral calculations of isobaric hot-spots created in Kr-doped implosions at the National Ignition Facility. The NN was trained on calculations of x-ray spectra using an isobaric hot-spot model post-processed with Cretin, a multi-species atomic kinetics and radiation code. The speedup provided by the NN model to generate x-ray emission spectra enables statistical analysis of parameterized models with sufficient detail to accurately represent the physical system and extract the plasma parameters of interest.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Star Formation in Splash Bridges

Splash bridges are created from the direct collision of two gas-rich disk galaxies. These direct collisions can eject gas masses on the order of 10 10 M ⊙ stripped from the stellar disks of each galaxy. The Taffy Galaxy system (UGC 1294/5) is a prototypical example of a splash bridge system. CO observations of the Taffy revealed that its splash bridge contains a mass of H 2 equal to the Milky Way's H 2 mass. However, the little visible star formation occurring within the bridge highlights the need for models of direct gas-rich disk collisions. The Arp 194 system displays what may be another splash bridge resulting from the collision between two disk galaxies. The region between the two stellar disks contains bright clumps of active star formation. We aim to better understand the conditions for star formation in splash bridges by employing a Jeans criterion to determine where gravitational instabilities occur in the shocked and cooling gas of gas-rich disk collisions. The splash bridge results are obtained from our previous work using a sticky particle code and post-processed. We find that the inclination between the gas disks and the collision velocity with which the gas collides strongly affects the fraction of gas that will become gravitationally unstable. Low inclinations between gas disks produce starbursts whereas high inclinations result in steady-rate star formation. The offset of the gas disks at impact will determine how many gas elements directly collide but does not strongly affect the resulting star formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

matsim-agents v1.0

matsim-agents is a multi-agent AI framework for atomistic materials simulation and discovery. It orchestrates large language models (LLMs), machine-learned interatomic potentials (MLIPs), and DFT codes into a single agentic loop running on laptops and DOE leadership-class supercomputers. MULTI-AGENT ORCHESTRATION A LangGraph state machine with three nodes: a Planner that converts a natural-language research objective into structured tasks; an Executor that dispatches atomistic tools and loops until the queue is empty; and an Analyst that summarizes results into a human-readable report. State is checkpointed after every step and human-in-the-loop gates can be inserted at any edge. HYPOTHESIS-DRIVEN DISCOVERY CHAT An interactive REPL (matsim-agents chat) that couples LLM dialogue with atomistic simulation. Chemical formulas are automatically detected in conversation turns and trigger a full crystal-phase exploration: structure generation → relaxation → stability scoring → result injection back into the conversation, creating a closed hypothesis-refinement loop. CRYSTAL PHASE ENUMERATION Given a composition, the phase explorer enumerates prototypes by stoichiometry: elemental (fcc/bcc/hcp/sc/diamond), binary 1:1 (rocksalt/CsCl/zincblende/ wurtzite/fluorite/rutile), ternary 1:1:3 (cubic perovskite), ternary 1:2:4 (perovskite + spinel), quaternary 1:1:2:6 (Fm-3m double perovskite). 2-D prototypes (graphene, h-BN, MoS2 2H/1T) and multilayer stacking are also supported via --include-2d and --num-layers. SUPERCELL GENERATION AND SITE DECORATION Auto-tiling to a minimum atom count (--min-atoms), explicit NxNxN tiling (--supercell), symmetry-distinct site decorations (--n-orderings), and isotropic lattice-scale sweeps (--lattice-scales) for volume bracketing. MLFF RELAXATION AND STABILITY SCORING HydraGNN (multi-headed GNN) drives structure relaxation via ASE with FIRE, BFGS, or BFGSLineSearch. Stability output: delta-E/atom ranking across phases and a max-residual-force dynamical-stability proxy. Other MLIPs (MACE, NequIP, Orb) can be plugged in through the same interface. DFT BACKENDS Quantum ESPRESSO pw.x and VASP 6.6 are first-class labellers. Both have validated GPU builds and SLURM/PBS launchers for three DOE platforms: Frontier (AMD MI250X, ROCm), Aurora (Intel PVC, oneAPI), Perlmutter (NVIDIA A100, CUDA). QE produces ~100 binaries (pw.x, ph.x, epw.x, ...). VASP supports scf, relax, vc-relax, and vc-relax-shape run types. ACTIVE-LEARNING LOOP matsim-agents al run CONFIG.yaml drives an iterative HydraGNN-DFT loop: MD generates candidates → ensemble/MC-dropout uncertainty selects the most informative → DFT labels them in parallel inside one allocation → dataset grows → HydraGNN retrains → repeat. DFT backend is a single YAML toggle (dft.backend: vasp | qe). LLM-generated seed structures are supported (no curated POSCAR library needed). Config uses ${VAR}, ${VAR:-default}, ${VAR:?msg} shell-style substitution for cross-user/cross-site portability. LLM BACKENDS Ollama (local, default), vLLM (HPC multi-GPU serving), OpenAI, Anthropic, HuggingFace Transformers+Accelerate. Selected at runtime via flag or env var with no code changes. HPC PORTABILITY Same Python entry points run on Frontier (ROCm 7.2), Aurora (oneAPI), and Perlmutter (CUDA 12). DFT and ML stacks are never co-loaded in the same shell; they couple through the scheduler and filesystem. Advanced multi-node launchers (serve, discovery-chat, single-relaxation, active-learning, QE warm-start) are provided for all three platforms. CODABENCH COMPETITION BUNDLE A self-contained benchmark: 159 atomistic test structures across 11 material classes, 5 tasks (formation energy, forces, ML relaxation, AI-DFT relaxation, phase stability ranking), public/private leaderboard split (30/70), and four ready-to-run baselines: MACE-MP-0, HydraGNN, UMA, AllScAIP.

Lupo Pasini, Massimiliano [Oak Ridge National Labo↗
DOE OSTI2024

A novel conjugative transposon carrying an autonomously amplified plasmid

Tetracyclines serve as broad-spectrum antibiotics to treat bacterial infections. The discovery of new tetracycline resistance genes has led to new questions about the underlying mechanisms of resistance, gene transfer, and their relevance to human health. We tracked changes in the abundance of a 55-kbp conjugative transposon (CTn214) carrying tetQ, a tetracycline resistance gene, within a Bacteroides fragilis metagenome-assembled genome derived from shotgun sequencing of microbial DNA extracted from the ileal pouch of a patient with ulcerative colitis. The mapping of metagenomic reads to CTn214 revealed the multi-copy nature of a 17,044-nt region containing tetQ in samples collected during inflammation and uninflamed visits. B. fragilis cultivars isolated from the same patient during periods of inflammation harbored CTn214 integrated into the chromosome or both a circular, multi-copy, extrachromosomal region of the CTn214 containing tetQ and the corresponding integrated form. The tetracycline-dependent mechanism for the transmission of CTn214 is nearly identical to a common conjugative transposon found in the genome of B. fragilis (CTnDOT), but the autonomously amplified nature of a circular 17,044-nt region of CTn214 that codes for tetQ and the integration of the same sequence in the linear chromosome within the same cell is a novel observation. Genome and transcriptome sequencing of B. fragilis cultivars grown under different concentrations of tetracycline and ciprofloxacin indicates that tetQ in strains containing the circular form remains actively expressed regardless of treatment, while the expression of tetQ in strains containing the linear form increases only in the presence of tetracycline.

59 BASIC BIOLOGICAL SCIENCES↗